MCP Tools Configuration
🌐 What is MCP?
MCP (Model Context Protocol) is like a universal connector that lets your AI agent access external tools and data—think of it as giving your agent superpowers to interact with the real world.
What MCP Does for Your Agent
Instead of just chatting, your agent can now:
📁 Read and write files in your project folders
🗄️ Query databases to fetch business data
📧 Send emails through Gmail or Outlook
💬 Post messages to Slack or Teams
🎫 Create tickets in Jira or Zendesk
🔍 Search code in GitHub repositories
📊 Fetch analytics from your business tools
🛒 Access CRM data from Salesforce or HubSpot
⚡ And 300+ more integrations
Why Use MCP?
Before MCP:
Agents could only chat and answer questions
No access to your files, databases, or business tools
Limited to what's in their training data
With MCP:
Agents take real actions in your systems
Access live data from your business applications
Automate workflows across multiple tools
Work with your actual project files and data
🔧 How MCP Works (Simple Explanation)
Think of MCP like adding apps to your smartphone:
MCP Servers = App Store apps (Gmail, Slack, GitHub, etc.)
MCP Connections = Installing and logging into apps
MCP Tools = Features within each app (send email, post message, search code)
Your Agent = The user who can now use these apps
Example Workflow:
You set up a connection to Gmail (like logging into Gmail on your phone)
Your agent can now access Gmail tools (send email, read inbox, etc.)
When a user asks "Send this to my team", the agent uses the Gmail tool
The email gets sent—just like you would do manually
🚀 Setting Up MCP Tools (2-Step Process)
Step 1: Create MCP Connections (One-Time Setup)
Before your agent can use MCP tools, you need to set up connections to the services you want to use.
Where to Set Up Connections
Go to your Project Settings
Click on Connections or Integrations
Click "Add Connection"
Select "MCP Client"
What You'll Configure
1. Name Your Connection
Give it a clear, descriptive name
Example: "GitHub Code Access", "Gmail for Support", "Analytics Database"
2. Enter Server URL
This is the address of the MCP server
Your provider or IT team will give you this URL
Example:
https://mcp.github.com/v1
3. Choose Transport Type
Streamable HTTP: Modern standard, recommended for all new connections
SSE (Server-Sent Events): Legacy method, being deprecated
If unsure, use Streamable HTTP
4. Set Up Authentication
You have two options:
Option A: No Authentication
For internal tools or public services
Just click "Save" and you're done
Option B: OAuth (Secure Login)
For services like Gmail, GitHub, Slack
Click "Initialize OAuth"
You'll be redirected to login (like "Sign in with Google")
Approve the permissions
AgenticFlow saves your login securely
Tokens refresh automatically—no need to re-login
5. Test Connection
Click "Test Connection"
You'll see a list of available tools
Green checkmark = Connection works!
Red error = Check your URL or authentication
Example: Setting Up Gmail
Name: Gmail for Customer Support
URL: https://mcp.gmail.com/v1
Transport: Streamable HTTP
Authentication: OAuth
→ Click "Initialize OAuth"
→ Login with your Google account
→ Approve email permissions
→ Done! ✓Step 2: Add MCP Tools to Your Agent
Now that connections are set up, configure which ones your agent can use.
In Agent Builder → Tab 5: MCP Tools
1. Click "Add MCP Client"
Select from your configured connections
You'll see all available tools from that service
2. Configure Tool Behavior
Run Behavior: How the agent uses tools
Auto Run (Recommended for most cases)
Agent automatically uses tools when needed
Best for: File reading, data queries, searches
Example: "Show me the latest sales data" → Agent queries database automatically
Request Confirmation (For sensitive actions)
Agent asks user before using tool
Best for: Sending emails, creating tickets, deleting files
Example: "Send email to client" → Agent asks "Should I send this email?" → User confirms
Timeout: How long to wait for tool response
Default: 150 seconds (2.5 minutes)
Increase for slow operations (large file processing, complex queries)
Decrease for quick operations (simple API calls)
3. Select Specific Tools (Optional)
By default, your agent can use all tools from the connection. You can customize:
Allow All Tools:
Leave tool selection empty
Agent can use any tool from this connection
Good when you trust all capabilities
Choose Specific Tools:
Toggle which tools the agent can use
Example: For GitHub, allow "search code" and "read file" but not "delete repository"
Prevents accidental destructive actions
4. Add Usage Instructions (Optional)
Tell your agent when and how to use these tools:
Example for File System:
Use these tools when users ask to read, write, or organize files in their project.
Always check if a file exists before trying to read it.
Ask for confirmation before deleting any files.Example for CRM:
Search customer records when users ask about account details or contact information.
Always create new leads when a potential customer is mentioned.
Update contact details when users provide new information.Example for Email:
Send emails only when explicitly requested.
Always show the draft to the user before sending.
Use professional tone in all email communications.🎯 Common MCP Tool Setups
Setup 1: Customer Support Agent
Goal: Agent handles support tickets and emails
MCP Connections Needed:
Gmail - Send and read customer emails
Zendesk - Create and update support tickets
Knowledge Base - Search help documentation
Agent Configuration:
MCP Client: Gmail
Run Behavior: Request Confirmation
Timeout: 60 seconds
Tools: Send email, read inbox, search messages
Instructions: "Always show email drafts before sending"
MCP Client: Zendesk
Run Behavior: Auto Run
Timeout: 90 seconds
Tools: Create ticket, update ticket, search tickets
Instructions: "Create tickets for all customer issues"
MCP Client: Knowledge Base
Run Behavior: Auto Run
Timeout: 30 seconds
Tools: Search articles, get article content
Instructions: "Search help docs before escalating to human"Setup 2: Development Assistant Agent
Goal: Agent helps with coding and project management
MCP Connections Needed:
GitHub - Access code repositories
Jira - Manage development tasks
File System - Read/write project files
Agent Configuration:
MCP Client: GitHub
Run Behavior: Auto Run
Timeout: 120 seconds
Tools: Search code, read file, list repositories
Instructions: "Help find code examples and explain implementations"
MCP Client: Jira
Run Behavior: Request Confirmation
Timeout: 60 seconds
Tools: Create issue, update issue, search issues
Instructions: "Create tickets for bugs, ask before updating existing tickets"
MCP Client: Project Files
Run Behavior: Auto Run
Timeout: 45 seconds
Tools: Read file, list directory (delete disabled)
Instructions: "Read project files when analyzing code structure"Setup 3: Sales & Analytics Agent
Goal: Agent provides business insights and manages leads
MCP Connections Needed:
Salesforce - CRM data and lead management
Analytics Database - Business metrics
Slack - Team notifications
Agent Configuration:
MCP Client: Salesforce CRM
Run Behavior: Request Confirmation
Timeout: 90 seconds
Tools: Search contacts, create lead, view opportunities
Instructions: "Look up customer details, create leads for new prospects"
MCP Client: Analytics Database
Run Behavior: Auto Run
Timeout: 120 seconds
Tools: Execute query, list tables
Instructions: "Query sales metrics, user statistics, and performance data"
MCP Client: Slack Notifications
Run Behavior: Auto Run
Timeout: 30 seconds
Tools: Post message, send to channel
Instructions: "Notify #sales channel for high-value leads"🛡️ Security & Permissions
Authentication Security
OAuth (Recommended):
Most secure method for cloud services
You login once, AgenticFlow handles the rest
Tokens stored encrypted
Auto-refreshes—no re-authentication needed
Can revoke access anytime from service settings
No Authentication:
Only use for internal/private tools
Good for tools on your private network
Not recommended for internet-facing services
Tool Permissions Best Practices
Grant Only What's Needed:
✅ DO: Enable "read file" for code review agents
❌ DON'T: Enable "delete file" unless absolutely necessary
Use Request Confirmation for:
Sending emails or messages
Creating/updating database records
Deleting any data
Making purchases or financial transactions
Publishing content publicly
Use Auto Run for:
Reading files or data
Searching and querying
Fetching information
Generating reports
Non-destructive operations
Monitoring & Safety
What AgenticFlow Tracks:
Every tool your agent uses
When tools are called and by which user
Success or failure of each tool call
Time taken for each operation
Review Agent Logs:
Check which tools are being used most
Identify failed tool calls
Monitor for unexpected behavior
Audit sensitive operations
🔍 Troubleshooting Common Issues
Issue: "Authentication Failed"
What it means: Agent can't connect to the MCP server
How to fix:
Go to Connection Settings → Find the MCP connection
Check if status shows "Not Authenticated"
For OAuth: Click "Re-authorize" and login again
For No Auth: Verify the server URL is correct
Click "Test Connection" to verify
Issue: "Tool Not Found"
What it means: Agent tries to use a tool that's not available
How to fix:
Go to Agent Builder → Tab 5: MCP Tools
Verify the MCP client is added to your agent
Check the tool name is spelled correctly
In tool selection, make sure the tool is enabled (toggled on)
Test the connection to see available tools
Issue: "Timeout Error"
What it means: Tool took too long to respond
How to fix:
Go to Agent Builder → Tab 5: MCP Tools
Find the MCP client configuration
Increase the Timeout value (try 200-300 seconds)
If still failing, contact your MCP server administrator
Consider if the operation is too complex (query too large, file too big)
Issue: "Permission Denied"
What it means: Agent doesn't have permission for this tool
How to fix:
Check if tool is enabled in agent configuration
For OAuth: Re-authorize with correct permissions/scopes
Verify your user account has permission in the external service
Check if IP whitelisting is needed for your MCP server
Issue: "Agent Doesn't Use Tools"
What it means: Agent answers questions but doesn't use MCP tools
How to fix:
Add instructions in MCP tool description
Update system prompt to mention when to use tools
Test directly: Ask "Can you read the file X?" (be explicit)
Check model selection: Some models are better at tool use (Claude, GPT-4)
Verify tools are enabled in agent configuration
📊 Monitoring Tool Usage
View Agent Activity
In Agent Dashboard:
See which tools were called in each conversation
View success/failure rates
Check average response times
Monitor token usage
In Connection Settings:
See when OAuth tokens expire
Check connection health status
View last successful connection
Test tools on-demand
Understanding Tool Performance
Good Performance:
Tool calls succeed > 95% of time
Response time < 5 seconds for most operations
OAuth tokens refresh automatically
No authentication errors
Needs Attention:
Success rate < 90%
Frequent timeout errors
Repeated authentication failures
Users complaining about slow responses
Optimization Tips:
Increase timeout for slow operations
Use caching when possible
Limit number of tools per agent (5-10 is ideal)
Remove unused MCP connections
Monitor during peak usage times
✅ Best Practices Checklist
Before Deployment
After Deployment
🎓 Tips for Success
Start Simple
Begin with 1-2 MCP connections
Test thoroughly before adding more
Add tools gradually based on actual needs
Don't overwhelm your agent with too many options
Name Things Clearly
Use descriptive connection names: "Gmail for Support" not "Connection 1"
Write clear usage instructions
Document what each tool does
Make it easy for future you to understand
Test Before Going Live
Use Chat Playground to test each tool
Try edge cases (empty results, errors, timeouts)
Verify confirmations work as expected
Check that errors are handled gracefully
Guide Your Agent
Add instructions for when to use tools
Include examples in system prompt
Mention tools in agent knowledge base
Be specific about use cases
Monitor and Improve
Check logs regularly
Look for patterns in tool usage
Identify and fix common errors
Adjust based on user feedback
🔗 Related Documentation
Visual Agent Builder Guide - Complete Tab 5 walkthrough with screenshots
Agent Configuration Overview - Understanding all 11 configuration tabs
Model Selection - Choosing the right AI model for tool use
Tools & Actions - Workflow-based tools vs MCP tools
Knowledge Base - Combining MCP tools with knowledge
📚 Learn More About MCP
What is MCP?
Visit modelcontextprotocol.io for the official guide
Universal standard for AI tool integrations
Created by Anthropic, adopted industry-wide
Open-source and extensible
Finding MCP Servers:
Browse official server directory
Search npm for
@modelcontextprotocol/*packagesCheck your service provider's documentation
Many popular tools have official MCP servers
Custom Integrations:
Contact AgenticFlow support for custom MCP server setup
Work with your IT team to deploy internal MCP servers
Request new integrations from the AgenticFlow team
Need Help?
In-App Support: Click the help icon in Agent Builder
Community: Ask in AgenticFlow community forums
Support Team: Contact [email protected]
Your agent's MCP tools transform it from a chatbot into a powerful automation assistant—configure thoughtfully, test thoroughly, and watch your agent handle real work! 🚀
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